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Gut Health Guide

Updated: Aug 2, 2022

The Importance of Gut Health


The gut, or gastrointestinal system, is truly a gateway to overall health.

The gut microbiome is an ecosystem of organisms including bacteria, yeasts, fungi, viruses, and protozoan throughout the digestive tract. Far beyond just digestive health, the following organ systems are also closely related to gut health:

  • Immune system

  • Endocrine system

  • Nervous system

  • Circulatory system

  • Integumentary system

  • Respiratory system

  • Reproductive system

A few key points to consider:

  • There is TEN TIMES the amount of bacteria in our body than our own cells and the majority of them are found within our digestive system.

  • The gastrointestinal system contains 90% of the body’s happy hormone, serotonin.

  • Most importantly, approximately 70% of our immune system is housed in our gut!

As you can tell, gut health doesn’t stop at digestion. The health of our gut affects nearly every system in our bodies!

What Is Leaky Gut?

Leaky gut is a term that refers to intestinal hyperpermeability and has become an increasingly more common health problem seen today. Leaky gut causes MAJOR health problems, including autoimmunity. How, though?

Intestinal hyperpermeability is exactly what it sounds like... the digestive tract is no longer able to ensure the good stays in and the bad stay out. Instead, the tight junctions, or the proteins holding the intestinal walls together, are loosened. This leaves sizable gaps for undigested food particles, digestive fluids, and toxins to enter the bloodstream.

The body reacts to these foreign particles in the blood by producing immune antibodies, or pro-inflammatory cells, to fight them off. This breeds chronic inflammation, food allergies, and various health complications. Of course, there are no signs of improvement until the gut’s permeability is addressed.


Fortunately, we now have a better understanding of the causes, obstacles, and treatment methods for leaky gut so there IS a stop to the cycle!


What causes leaky gut?

Several factors have proved to negatively affect the gut’s integrity. The most prominent include:

  • The Standard American Diet - Exposure to Chemicals

  • Chronic Infections

  • Gluten and Other Grains

  • Food Allergies

  • Excessive Medications

  • Poorly Managed Stress

The Standard American Diet, rightfully known as the SAD diet, is one of the leading causes of the chronic health issues we see today. According to a recent study conducted by the USDA, 63% of the calories Americans are consuming came from processed foods containing preservatives, refined grains, and added sugars and oils. It’s almost as though the general public took it upon themselves to refigure the food pyramid to consist of:

  • Processed grain at the base


  • Processed dairy in the middle


  • And sugar at the top

When in all honesty, none of these foods have any business being part of our diets at all.


A couple of alarming facts:

  • The United States Food and Drug Administration (FDA) has approved approximately 3,000 different food additives, preservatives, and colorings without adequate research on safety!

  • The average person ingests over 150 pounds of additives each year!

  • The magnitude that these chemicals are allowed into our lives is incomprehensible. We are becoming more and more aware of the consequences of this fake-food lifestyle and it is simply unacceptable! This is only one factor in the leaky gut epidemic, but definitely a big one! Up next, we will be discussing other factors responsible for the onset and progression of leaky gut.


Address Gluten


Gut Health and Inflammation


Inflammation is a vital immune response and is the body’s attempt to defend itself against pathogens, heal from injury, and repair damaged tissue. Chronic inflammation, however, is not beneficial to our bodies in any way. In fact, it can worsen the body’s ability to recognize foreign invaders and puts the body in a state of stress for extended periods of time. This can cause lasting damage, increased food allergies, and eventually autoimmunity. This type of inflammation can be caused by a number of things, but largely seen as a result of leaky gut syndrome and poor dietary habits. If chronic inflammation goes untreated, leaky gut is worsened and the body ultimately loses its ability to repair from the damage.


Gluten On The Gut

Gluten is the general term for a mix of proteins in many grains such as wheat, barley, and rye. Gluten has found itself in much of our food supply, disguised in packaged foods and featured in most pre-prepared dishes. It is no surprise that our consumption of gluten has increased immensely and our health is suffering from it.

Gluten allergies, sensitivities, and intolerances are becoming increasingly more common, “gluten-free” has become a buzz word within the health community, and people are finally beginning to explore how dangerous gluten can be for their health.


How can it be dangerous?

Gluten makes your gut leaky. Simple as that. Zonulin, a protein found in gluten, increases the permeability of the gut by further opening the spaces between cells. The antibodies normally released as a result of leaky gut are accompanied by MORE antibodies created to attack one of the gluten’s more prominent building blocks, gliadin. This leads to more inflammation, more bodily confusion, and more health complications.

In other words, your body reacts to the consumption of gluten by creating a defense mechanism to fight it. Once this damage has occurred within the digestive tract, it is then distributed throughout the entire body.


Aside from contributing (if not entirely causing) leaky gut, gluten increases inflammation, overall digestive distress AND alters the balance of our microbiome. Our microbiome must be equipped with efficient healthy bacteria in order to be successful in carrying out its necessary functions.

Without the proper balance of bacteria, the following functions are disrupted:

  • Digestion

  • Immune response

  • Nutrient absorption

  • Hormone regulation

  • Vitamin production

  • Detoxification

  • Mood management

  • And many more


Gluten produces both primary and secondary effects.

The damage gluten causes that we have talked about thus far has mostly been the primary effects:

  • Intestinal hyperpermeability (leaky gut)

  • Permeability of the blood-brain barrier

  • The onset of autoimmune diseases (such as celiac disease, Crohn's, and ulcerative colitis)

  • The development of psychological disorders

  • Dysbiosis, or abnormal bacteria growth

  • Acute allergic, or IgE, responses and a delayed antibody response

While all of these issues are very serious within themselves, they, too, cause further complications. Now onto the secondary effects of gluten...


The secondary effects of gluten exposure include:

  • Severe nutrient deficiencies (such as iron and vitamin B12)

  • Systemic inflammation (leading to organ and tissue breakdown)

It may seem a bit redundant that we keep coming back to how your body acts on gluten, but it is one of the most important pieces of information you can take from this class! Gluten is a major component of the leaky gut cycle. It is present in the onset, the maintenance, and the progression of this damaging condition and it should not be taken lightly.


As you can probably guess, gluten’s path to disease is pretty direct. The first step is when gluten’s contribution goes unnoticed.


At this point, it is likely there are little to no known symptoms. This is where most people will assume that gluten won’t hurt them and therefore can eat it no problem. Unfortunately, the lack of apparent symptoms does not mean that gluten doesn’t hurt your gut. In fact, it takes exposure over time and the accumulation of damage before leaky gut will be noticeable. For those cutting out gluten before they feel any physical discomfort, they are still treating an underlying issue even if they can’t quite feel it yet.

The next step is the progression of subclinical problems. This is where leaky gut truly begins to develop. Often, the first thing that will be noticed is increased food and environmental allergies. Digestive distress may begin to become more frequent. Unfortunately, it is common for people to still avoid blaming gluten for their discomfort.

The last step is recognizing the problem. However, it is not usually recognizing gluten as the problem, but the acknowledgment of the problem that gluten has caused. For example, if someone is diagnosed with a chronic disease, or develops inflammatory changes, most medical doctors will begin treating these conditions rather than examining the origin.

It’s a shame that this happens so often as if gluten was recognized as the main problem during the early stages, then a lot of these health issues could be avoided entirely. Gluten, however, is not the only concern when it comes to solving leaky gut.



Address Conventional Dairy

Conventional cows milk is another food that can contribute to leaky gut. The component of dairy that will harm your stomach is the protein A1 casein. While some people can tolerate A1 casein, for others it acts as a trigger for lymphatic congestion, metabolic suppression, and weight gain. It can also cause major digestive problems, and not because of the lactose. It’s because of the massive histamine release from casomorphin (a protein). Additionally, the pasteurization process will destroy vital enzymes, making sugars like lactose very difficult to digest. Finally, most of the dairy products out on the market are made from animals who are fed loads of antibiotics, and as we know, antibiotics are awful for the gut. If you do eat dairy, stick to goat, sheep, or buffalo milk products, and whenever you can, try to find products that are high quality, organic, grass-fed, rBGH free, and preferably raw.


Say No to Pesticides


Much like the additives and preservatives flooding our food supply, pesticides are also a big part of what’s on our plates. There are THREE MILLION TONS of pesticides used worldwide each year and more than 16,000 chemicals involved in the production of these pesticides. Studies to ensure their safety on humans have been very limited, whereas some have no documented research at all! While we are not entirely sure of their safety on human health, we do recognize strong links between pesticide exposure and:

  • Nervous system disorders

  • Immune system suppression

  • Reproductive damage

  • Hormonal imbalances

  • Thyroid Issues

  • Type 2 Diabetes

  • Obesity

  • Asthma

  • Migraine headaches

  • Attention disorders

  • and developmental delay in children

The magnitude that pesticides (along with the steroids, hormones, antibiotics, and excitotoxins) show up in our food supply is truly frightening and to think it isn’t a main component of our leaky gut trend is simply impossible. 



3. Understand the interaction between drugs and the gut microbiome

Medication is severely overprescribed in the current medical model used today.


Medical programs train doctors to medicate symptoms, even when they are unsure of the cause. This, in the short term, has seemed to work because the patients experience temporary relief from their discomfort. But... what isn’t taken into account is how these excessive prescriptions have affected our bodies.

For example, statins, drugs used to lower cholesterol, have been shown to lower Vitamin D and coQ10 levels. While it may be lowering cholesterol, it is simultaneously causing nutrient deficiencies, muscle fatigue, increased blood pressure, and weakened immunity.

Painkillers (like ibuprofen, naproxen, and aspirin) contribute to Vitamin C and iron deficiencies leaving one vulnerable to disease AND eroding the mucosal lining of the stomach.

Acid reduction medications hinder the digestion of protein, calcium, and vitamin B12, often causing chronic pain and gut issues.

Long term use of antidepressants, too, significantly impacts the gut’s motility and causes digestive issues.

Lastly, it’s important to note that almost all medications are unable to differentiate between the good bacteria in our gut and the illness it is trying to attack. That results in an altered microbiome and a much greater risk of infections.

As you can tell, drugs offer a lot of unintended consequences that can affect our health very badly.

That said, there are obviously situations where drugs should be your solution, such as a life-threatening infection or a surgical situation. However, without the immediate emergency needs of medication, it is best to treat the issue than it is to temporarily patch the problem.


Depression and The Gut


Depression can't be overcome with a single solution, but some relief can be found in your gut. The gut and the brain communicate closely with one another, so when your gut is in trouble, it can trigger neurological symptoms like depression, anxiety, and migraines. This understanding of the connection between the brain and the gut is nothing new, think about the phrase “butterflies in your stomach,” which we associate with feeling nervous or anxious. These physical feelings based on your mental state prove the link between your gut and mind. Your gut bacteria manufacture 95 percent of the body’s supply of serotonin, an important ‘feel-good’ chemical. So if your gut is out of whack, the production of this chemical is also affected.

Our gut has 5 critical elements, or defenses, that it truly needs for healthy gut function. In order from the outermost layer of defense, they include:

  • Mucosal IgA Otherwise known as immunoglobulin A, this antibody found in the mucous membranes is considered your gut’s first line of defense against toxins.

  • Tight Junctions These are small proteins that are responsible for holding the gut’s cells together. This is what is most directly affected by leaky gut syndrome.

  • Gastro Associated Lymphoid Tissue (GALT) This is the gut’s concentrated immune system and in fact, 70% of our immune system altogether. This the gut’s last and most powerful layer of defense.

The gut’s accessory defenses include:

  • Friendly Bacteria As we mentioned, we have more bacteria in our bodies than we do our own cells. This bacteria can communicate with the GALT warning it of potential danger.

  • Stomach Acid This is absolutely essential for the digestion, absorption of nutrients, and defense against infections.

If there is any dysfunction throughout your gut’s line of defense, these five primary barriers need to be evaluated in order to heal and be treated properly.


Fixing Your Gut With A Functional Approach

The first step of healing is ruling out the fundamental causes of leaky gut. It’s important to recognize that it is very rarely ONLY one cause, but a combination of several causing the damage. You must first rule out, or begin to recognize, the following:

  • Vitamin deficiencies by functional nutrition testing

  • Infectious pathogens by blood and GI tract tests

  • Heavy metal toxicity by urine or hair testing

  • Gluten sensitivity through HLA-DQ genetic testing

  • Environmental allergies via skin or blood tests

If any of these come back positive, you have your first step of instructions: address the deficiencies, implement dietary changes, limit exposure to allergens, and consider detoxification methods. Once you have a better understanding of your body’s unique needs, you can begin the formal functional medicine protocol: The 4 R’s.


The 4 R program is administered to help you heal from digestive distress, reverse gut complications, and rebalance your gastrointestinal microbiome. It is an incredible tool to acknowledge and treat health issues, dysfunctions, imbalances, and personal health needs. It is done in the following order:

REMOVE: Eliminate problem foods, toxins, low-grade infections, and oxidative stress. REPAIR: Begin reintroducing a clean diet with essential nutrients your body needs. RESTORE: Repopulate your gut with healthy bacteria to restore the proper balance of gut flora. REPLACE: Replace digestive enzymes, antioxidants, and immune-boosting vitamins to promote sustainable and healthy digestion.

As functional medicine practitioners we are trained in this protocol and enthusiastic about making sure your individualized needs are addressed during the process.


1. Remove the bad: At this point, you may have already removed things you already knew were to be detrimental to your health, such as gluten and known allergies, but you’ll also want to remove much of the chemical burden in your daily life. This includes:

  • Pesticides on foods

  • Genetically modified organisms

  • Unnecessary medications

  • Unnatural household cleaners

2. Once you have an understanding of what should be removed from your daily life and you have begun to implement those changes, it is time to begin repairing the damage that had previously been done. This is done by calming chronic inflammation and reintroducing nutritious foods, digestive enzymes, probiotics, essential fiber, vitamins, minerals, and acids.

For some people, these steps may mean implementing intermittent fasting, supplementation, or personalized diet plans that cater to their specific health needs.

Again, be sure to consult with a practitioner to be sure you are beginning the most appropriate repair route for YOUR needs.

Supplements To Consider


Nutrients must be replaced for effective healing. While everyone’s needs are highly individualized, here are some common supplements that have been proven to be helpful in the gut healing process:

  • Probiotics

  • Prebiotics

  • Digestive Enzymes

  • Fiber

  • Collagen

  • Turmeric

  • L-glutamine

  • Quercetin

(These are ONLY suggestions. I'm unable to prescribe these supplements to you without comprehensive testing as everyone’s nutritional needs vary!)


However, the main take away from this is that you should not rely solely on supplements. They can be used to help your healing process, but the goal is to be able to sustain wellness with whole foods and healthy lifestyle choices long term without the need for piles of pills.


If I were to suggest ONE supplement to mix into your routine right now it would be Gut Food, created by one of my all-time favorites and a leader in Functional medicine, Dr. Hyman.



I have no affiliation with this company. Gut food is packed with prebiotics, probiotics, and polyphenols. It is shown to significantly improve overall gastrointestinal wellness.



Just Thrive: Gut healing supplements.

Get 15% OFF with code: CARLYREED










Think of probiotics as the roof that you put in after laying down a solid foundation. Probiotics come in after you’ve started removing and replacing the offending foods in your diet, only then will your gut start benefiting from the good bacteria that probiotics bring.

Healthy gut flora brought about by probiotic use can support leaky gut because it helps our bodies break down food and turn them into nutrients. They also assist in the secretion of inflammatory mediators and help produce a protective layer of mucus that makes nutrients more accessible for digestion.

Picking out your probiotic: Start with a high dose, something like 100 billion CFU’s per day (it should have a count right on the front of the package). Long term, you can cut back to 40 billion per day.

Know that probiotics decrease in potency over time, so keep them refrigerated to help them stay alive longer.

Take your probiotic in the morning when you wake up and just before you eat breakfast, studies show that survival rates are higher when taken before a meal rather than after eating. Additional findings report that survival rates were highest when the meal eaten contained some fat (avocado’s anyone?).Probiotics aren’t just found in pill form; they’re also naturally created through fermentation in foods that you can find throughout your local grocery store.

Sauerkraut - made from just cabbage and salt, delivers a healthy dose of probiotics and fiber. You can make your own, or buy it at the store, look for the refrigerated options- the shelf-stable varieties won’t have the same health benefits.

Kimchi - similar to German sauerkraut, it’s also made with cabbage but has a bit more of a kick with additional ingredients such as red pepper, ginger, and garlic. It’s delicious with eggs and makes for a great side dish to spice up veggies, rice, or soup, too. Kefir - it’s like a drinkable yogurt that’s a little bubbly. Be sure to buy the unflavored kind WITHOUT all the added sugars. If you’re not a fan of the taste of plain kefir on its own, blend it into a smoothie with berries and coconut milk. Tempeh - made from naturally fermented soybeans, tempeh is packed with essential amino acids and probiotics. It has a firm, crumbly texture and a nutty profile making it great for marinating and grilling/baking or crumbling up in a sauce as a meat replacement.

A quick note on yogurt: All too often, we see people at the grocery store who are trying to fill their carts with healthy food but simultaneously stack cartons of fruit-flavored yogurt atop their almond milk and seed crackers. Please know this, the folks who market that yogurt to you might slap the word “probiotic” onto the label, but with all the sugar that the yogurt contains, it’s doing more harm than good. Opt for plain yogurt, and add a drizzle of honey and some fresh or frozen fruit, instead.

Amp Up Your Collagen:


By now, you’ve probably heard about bone broth - it’s exactly what it sounds like, a broth made from hours of boiling and simmering animal bones, tendons, ligaments, marrow, skin, and other connective tissue: the result, a healing, nutrient-dense elixir that’s present in every health food store around the country. What makes bone broth so good for you is the high amounts of collagen and gelatin, which are packed with immune-boosting properties, amino acids, and gut lining support. Plus, because of its warm liquid form, it’s super easy for the body to digest and take in nutrients. My favorite brand of Bone Broth to buy is Fond (I have no affiliation with the company).


To make bone broth, place chicken, beef, or pork bones along with onion peels, carrot peels, parsley bits, and celery ends into a slow cooker. Then fill the slow cooker with water and about a teaspoon of salt. Then add two tablespoons of apple cider vinegar. Cook on low for at least 18 hours up to 72 hours. This broth can be used as a base for soups, to cook with rice, or as a drink on its own. And if you abstain from eating animal products, no worries! There are plenty of collagen supplement powders that can be added to smoothies and various recipes.


Right now, my favorite brand of collagen powder is Further Food. I have no affiliation with them either.









Address Stress With Meditation


Stress hormones attack and break down the tight junctions that line your digestive tract. When you reduce stress hormones through rest and relaxation, you can help rebuild these “leaks” and start to heal your gut. One of the best, and scientifically proven, ways to lower your stress is through meditation. However, we understand asking a beginner to sit down and have an “empty mind,” is a lot to ask. If you’re new to meditation or haven’t had any luck with it thus far, here are a few techniques you can try out: Mindfulness meditation: This type of practice encourages allowing your mind to wander, while simultaneously being observant of your thoughts -- without judging them. Over time, the goal is to become aware of patterns and tendencies. Perhaps you’ll notice that each time you come face-to-face with a mirror, you have a negative thought. From here, you’ll be able to make sure to catch yourself in the future and switch that negative thought to a positive one, thereby cutting back on stressors. Concentration meditation: This practice involves focusing your attention on a single point. To practice this, light a candle and stare at the flame for a few minutes. Add a mantra or listen to a meditative soundtrack onlin

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